{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T11:33:57Z","timestamp":1762860837187,"version":"build-2065373602"},"reference-count":138,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Epigenomes"],"abstract":"<jats:p>Background: Trait convergence or parallelism is widely seen across the animal and plant kingdoms. For example, the evolution of eyes in cephalopods and vertebrate lineages, wings in bats and insects, or shark and dolphin body shapes are examples of convergent evolution. Such traits develop as a function of environmental pressures or opportunities that lead to similar outcomes despite the independent origins of underlying tissues, cells, and gene transcriptional patterns. Our current understanding of the molecular processes underlying these phenomena is gene-centric and focuses on how convergence involves the recruitment of novel genes, the recombination of gene products, and the duplication and divergence of genetic substrates. Scope: Despite the independent origins of a given trait, these model organisms still possess some form of epigenetic processes conserved in eukaryotes that mediate gene-by-environment interactions. These traits evolve under similar environmental pressures, so attention should be given to plastic molecular processes that shape gene function along these evolutionary paths. Key Mechanisms: Here, we propose that epigenetic processes such as histone-modifying machinery are essential in mediating the dialog between environment and gene function, leading to trait convergence across disparate lineages. We propose that epigenetic modifications not only mediate gene-by-environment interactions but also bias the distribution of de novo mutations and recombination, thereby channeling evolutionary trajectories toward convergence. An inclusive view of the epigenetic landscape may provide a parsimonious understanding of trait evolution.<\/jats:p>","DOI":"10.3390\/epigenomes9040045","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T10:56:27Z","timestamp":1762858587000},"page":"45","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Convergent Evolution and the Epigenome"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5866-4043","authenticated-orcid":false,"given":"Sebastian Gaston","family":"Alvarado","sequence":"first","affiliation":[{"name":"Department of Biology, Queens College, City University of New York, 65-30 Kissena Blvd, Flushing, NY 11361, USA"},{"name":"Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7891-6893","authenticated-orcid":false,"given":"Annaliese","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Biology, Queens College, City University of New York, 65-30 Kissena Blvd, Flushing, NY 11361, USA"},{"name":"Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4598-1012","authenticated-orcid":false,"given":"Maral","family":"Tajerian","sequence":"additional","affiliation":[{"name":"Department of Biology, Queens College, City University of New York, 65-30 Kissena Blvd, Flushing, NY 11361, USA"},{"name":"Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.tree.2007.09.011","article-title":"Convergence and Parallelism Reconsidered: What Have We Learned about the Genetics of Adaptation?","volume":"23","author":"Arendt","year":"2008","journal-title":"Trends Ecol. 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